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Sample GSM127104 Query DataSets for GSM127104
Status Public on Mar 01, 2007
Title ICC3996 SA-treated 03 hpt
Sample type RNA
 
Channel 1
Source name Control
Organism Cicer arietinum
Characteristics Genotype: ICC3996
Age: 14 days (seedling)
Tissue: Shoot (stem and leaf)
Treatment protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Growth protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Extracted molecule total RNA
Extraction protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Label Cy3/Cy5
Label protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
 
Channel 2
Source name Treatment
Organism Cicer arietinum
Characteristics Genotype: ICC3996
Age: 14 days (seedling)
Tissue: Shoot (stem and leaf)
Treatment protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Growth protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Extracted molecule total RNA
Extraction protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Label Cy3/Cy5
Label protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
 
 
Hybridization protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Scan protocol See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
Description The data submitted represents the mean data from three biological replications that inlcuded dye swaps between control and treatment samples
Data processing See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted
 
Submission date Aug 11, 2006
Last update date Mar 01, 2007
Contact name Tristan Coram
E-mail(s) tristan.coram@ars.usda.gov
Organization name USDA-ARS, NC State University
Street address 4118 Williams Hall, NC State University
City Raleigh
State/province NC
ZIP/Postal code 27695
Country USA
 
Platform ID GPL4079
Series (1)
GSE5512 Chickpea genes regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid

Data table header descriptions
ID_REF
VALUE Log (base 2) transformed mean expression ratio of treatment/control
FLAG Quality control where 0 indicates a good spot and 1 is a bad spot
ICC3996 SA 03hpi pairMean ratio Non-transformed mean expression ratio
ICC3996 SA 03hpi pairBG Mean ratio Non-transformed mean background ratio
ICC3996 SA 03hpi pairMedian ratio Non-transformed median expression ratio
ICC3996 SA 03hpi pairBG Median ratio Non-transformed median background ratio
ICC3996 SA 03hpi (control)Mean Non-transformed control channel mean
ICC3996 SA 03hpi (control)BG Mean Non-transformed control channel background mean
ICC3996 SA 03hpi (control)Median Non-transformed control channel median
ICC3996 SA 03hpi (control)BG Median Non-transformed control channel background median
ICC3996 SA 03hpiMean Non-transformed treatment channel mean
ICC3996 SA 03hpiBG Mean Non-transformed treatment channel background mean
ICC3996 SA 03hpiMedian Non-transformed treatment channel median
ICC3996 SA 03hpiBG Median Non-transformed treatment channel background median
ICC3996 SA 03hpi pairMean ratio cv Non-transformed mean expression ratio coefficient of variation
ICC3996 SA 03hpi pairBG Mean ratio cv Non-transformed mean background ratio coefficient of variation
ICC3996 SA 03hpi pairMedian ratio cv Non-transformed median expression ratio coefficient of variation
ICC3996 SA 03hpi pairBG Median ratio cv Non-transformed median background ratio coefficient of variation
ICC3996 SA 03hpi (control)Mean cv Non-transformed control channel mean coefficient of variation
ICC3996 SA 03hpi (control)BG Mean cv Non-transformed control channel background mean coefficient of variation
ICC3996 SA 03hpi (control)Median cv Non-transformed control channel median coefficient of variation
ICC3996 SA 03hpi (control)BG Median cv Non-transformed control channel background median coefficient of variation
ICC3996 SA 03hpiMean cv Non-transformed treatment channel mean coefficient of variation
ICC3996 SA 03hpiBG Mean cv Non-transformed treatment channel background mean coefficient of variation
ICC3996 SA 03hpiMedian cv Non-transformed treatment channel median coefficient of variation
ICC3996 SA 03hpiBG Median cv Non-transformed treatment channel background median coefficient of variation

Data table
ID_REF VALUE FLAG ICC3996 SA 03hpi pairMean ratio ICC3996 SA 03hpi pairBG Mean ratio ICC3996 SA 03hpi pairMedian ratio ICC3996 SA 03hpi pairBG Median ratio ICC3996 SA 03hpi (control)Mean ICC3996 SA 03hpi (control)BG Mean ICC3996 SA 03hpi (control)Median ICC3996 SA 03hpi (control)BG Median ICC3996 SA 03hpiMean ICC3996 SA 03hpiBG Mean ICC3996 SA 03hpiMedian ICC3996 SA 03hpiBG Median ICC3996 SA 03hpi pairMean ratio cv ICC3996 SA 03hpi pairBG Mean ratio cv ICC3996 SA 03hpi pairMedian ratio cv ICC3996 SA 03hpi pairBG Median ratio cv ICC3996 SA 03hpi (control)Mean cv ICC3996 SA 03hpi (control)BG Mean cv ICC3996 SA 03hpi (control)Median cv ICC3996 SA 03hpi (control)BG Median cv ICC3996 SA 03hpiMean cv ICC3996 SA 03hpiBG Mean cv ICC3996 SA 03hpiMedian cv ICC3996 SA 03hpiBG Median cv
Blank1 1 1.7559 2.4863 1.9537 2.7031 1535.7393 805.9336 1252.1667 724.5556 2863.5624 2473.7483 2704.4722 2442 0.4745 0.5447 0.4595 0.5682 0.5857 0.5403 0.5759 0.5412 0.5713 0.6954 0.605 0.7024
Blank2 1 2.4669 2.7381 2.6458 2.982 837.6635 712.3797 762.8056 642.8056 2500.1012 2394.9988 2454.9167 2364.2222 0.5887 0.5833 0.6056 0.5948 0.5388 0.5277 0.555 0.525 0.7041 0.6979 0.7139 0.6999
Blank3 1 2.4541 2.6204 2.6033 2.7996 1224.3671 745.2251 943.6111 679.8333 2982.6896 2438.1885 2726.3611 2385.1111 0.5437 0.5392 0.5802 0.5605 0.7257 0.5257 0.4745 0.5302 0.5479 0.7064 0.6409 0.7083
Blank4 1 2.2365 2.6694 2.4193 2.922 987.9668 726.2272 908.4722 656.25 2624.6427 2405.7338 2615.8611 2372.3333 0.5468 0.5656 0.5756 0.592 0.6234 0.5403 0.645 0.5344 0.6993 0.7004 0.7084 0.702
CA0009 0.7388 0 2.8308 2.3396 3.1737 2.6944 33893.8504 1010.1543 40838.3611 778.8333 33951.7729 2923.7966 38701.4722 2642.7222 1.0234 0.5076 1.0938 0.541 0.6885 0.6042 0.7022 0.5646 0.4487 0.7206 0.4313 0.7206
CA0011 NORMCON2 0.0287 0 1.0027 2.2599 1 2.4541 50342.094 1104.4465 65535 912.4722 50555.8272 2763.4776 65535 2603.8056 0.0413 0.536 0 0.56 0.0923 0.6519 0 0.5829 0.1133 0.656 0 0.6746
CA0014 0.2087 0 1.2082 2.5496 1.2248 2.7462 5872.5492 805.41 5964.6111 733.4444 8186.0901 2568.3802 8398 2518 0.4573 0.5406 0.4749 0.5718 0.402 0.5381 0.4009 0.5366 0.6522 0.7059 0.6603 0.7095
CA0015 -0.1305 0 1.3718 2.6094 1.4117 2.8332 8949.3484 824.4609 8281.7778 727.4722 11619.5854 2638.7732 11120.6389 2590.9167 0.1448 0.549 0.1595 0.5659 0.7878 0.5392 0.7639 0.5319 0.7702 0.7099 0.7541 0.7216
CA0018 NORMCON3 1 1.0813 2.7123 1.0922 2.9286 3918.5438 761.2007 3988.0278 684.4167 3997.6601 2539.1458 3949.9444 2499.4167 0.4838 0.56 0.5016 0.5847 0.1614 0.4962 0.2326 0.5072 0.4163 0.7028 0.3972 0.7145
CA0020 NORMCON4 0.0283 0 1.0247 2.3612 0.9823 2.5791 49200.2232 951.1549 64313.0833 818.5556 50415.3803 2732.5406 63242.2778 2610.5278 0.111 0.5258 0.1131 0.5655 0.1013 0.5691 0.041 0.5504 0.1417 0.6903 0.1236 0.6962
CA0021 0.5958 0 1.9756 2.5276 2.4837 2.7363 39717.7156 819.6818 47736.9444 722.4444 50487.3721 2572.4159 65273.1667 2472.1944 0.7268 0.5279 0.8882 0.5586 0.5314 0.5315 0.5431 0.5273 0.142 0.7037 0.017 0.71
CA0030 -0.0168 0 1.2797 2.5409 1.2876 2.798 35173.9295 867.8701 44085.4722 731.7222 36704.2359 2656.4103 44189.3611 2536.5 0.3601 0.5534 0.4178 0.5694 0.5753 0.5383 0.6 0.5349 0.4726 0.6994 0.4911 0.7099
CA0032 -0.716 0 0.8829 2.4976 0.844 2.8441 23899.1121 813.2035 27159.8333 692.5 19291.9149 2550.7536 20587.5833 2477.8611 0.178 0.5388 0.1766 0.5694 0.7213 0.5404 0.757 0.5156 0.6944 0.7064 0.7037 0.7071
CA0036 -0.1725 0 1.2986 2.4268 1.3112 2.7431 30450.8059 979.6462 37306.8056 802.3333 24669.5165 2826.6504 28443.8889 2719.5 0.6438 0.5307 0.7078 0.5689 0.6529 0.5867 0.6699 0.5446 0.5081 0.69 0.4995 0.7024
CA0043 0.0052 0 1.5384 2.5776 1.5657 2.7277 8763.5125 930.0446 9271.4167 842.5 8855.3885 2793.8111 9016.0556 2702.0278 0.5878 0.5651 0.6378 0.6007 0.6406 0.6449 0.655 0.6611 0.4429 0.6838 0.44 0.6928
CA0049 -0.0356 0 1.3976 2.5589 1.4174 2.8026 24250.0347 920.7054 27752.5833 794.0278 21024.6208 2869.1077 23250.0278 2743.0556 0.6287 0.5509 0.6674 0.5888 0.6962 0.5613 0.7205 0.5477 0.5521 0.696 0.5645 0.7041
CA0106 -0.035 0 1.5189 2.5946 1.572 2.8142 3708.1043 838.4471 3556.5278 748.5 5284.0011 2670.8715 5208.7222 2614.9722 0.1721 0.559 0.178 0.5883 0.5597 0.541 0.5585 0.5383 0.5053 0.697 0.4984 0.7048
CA0108 -0.7369 0 0.8704 2.5707 0.8382 2.7921 11451.1989 872.176 12323.1111 779.8889 9487.7281 2788.5188 9774.8889 2730.3889 0.141 0.5576 0.1515 0.5711 0.6724 0.5368 0.6863 0.5342 0.6642 0.7005 0.6791 0.7041
CA0112 0.3306 0 1.8253 2.3962 1.8551 2.5465 9188.6952 949.3295 9649.75 859.0833 10595.8991 2799.9219 10844.25 2719.8333 0.6184 0.5251 0.6578 0.5598 0.6591 0.5749 0.6651 0.57 0.4452 0.6962 0.4363 0.7042
CA0178 -0.6532 0 0.8248 2.385 0.7958 2.7336 36023.2487 952.9133 42724.3056 764.3889 26929.374 2777.5661 30203.8056 2609.6667 0.2768 0.5436 0.319 0.5683 0.4006 0.5624 0.4161 0.5278 0.2558 0.7085 0.2521 0.7128

Total number of rows: 727

Table truncated, full table size 142 Kbytes.




Supplementary file Size Download File type/resource
GSM127104 ICC3996 03h SA control (cy3) rep1 TXT.txt.gz 593.6 Kb (ftp)(http) TXT
GSM127104 ICC3996 03h SA control (cy5) rep2 TXT.txt.gz 586.6 Kb (ftp)(http) TXT
GSM127104 ICC3996 03h SA control (cy5) rep3 TXT.txt.gz 585.3 Kb (ftp)(http) TXT
GSM127104 ICC3996 03h SA treated (cy3) rep2 TXT.txt.gz 592.5 Kb (ftp)(http) TXT
GSM127104 ICC3996 03h SA treated (cy3) rep3 TXT.txt.gz 590.6 Kb (ftp)(http) TXT
GSM127104 ICC3996 03h SA treated (cy5) rep1 TXT.txt.gz 589.9 Kb (ftp)(http) TXT

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